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Fig. 7.3
.
Mobilities in global modes shown by color-coded diagrams for KcsA.
(a) The different
regions of the protein are indicated, namely, the inner and outer helix (TM1 and TM2 respectively),
the putative intracellular gate, the selectivity filter and the turret region. (b) The slowest global
mode (mode type I), which is two fold degenerate (top), is an opening/stretching motion, with the
turrets opening and closing above the selectivity filter. The second lowest frequency mode (mode
type II) (bottom), corresponds to a twisting/torsion motion, leading to a widening of the pore,
shown in the next panel. (c)
Pore-radius profiles (top panel) as a function of the position along the
cylindrical (Z-) axis. Bottom panel shows a solid-sphere representation of the inner surface of the
channel at the pore region for the crystal structure (left), for the model of the open form (right).
The color code for the solid-sphere representation of the pore region is: red, pore radius < 1.15 Å;
green, 1.15 Å < radius < 2.30 Å; and blue, radius > 2.30 Å. The pore radius profiles were generated
using HOLE (Smart
et al.
, 1993).
In the inset of panel (c) is the backbone of the crystal structure
(blue) superimposed onto the model of the open form (red). Two monomers have been deleted for
clarity.
sequences and pore region structures of these five channels. The observed
structural similarities in the pore-forming region suggested a common gating
mechanism, which was indeed verified by GNM/ANM calculations. The
equilibrium dynamics of these five channels were found to obey similar patterns
on a global scale. Mainly, two types of highly cooperative motions were
identified at the low frequency end of the mode spectrum, shared by all five
structures: The first (referred to as type I) is an alternating expansion/contraction
of the EC and/or CP via anti-correlated fluctuations of oppositely located pairs of
